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Open data
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Basic information
Entry | Database: PDB / ID: 4oqu | ||||||
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Title | Structure of the SAM-I/IV riboswitch (env87(deltaU92)) | ||||||
![]() | SAM-I/IV riboswitch | ||||||
![]() | RNA / riboswitch / aptamer / pseudoknot / regulation / S-adenosylmethionine | ||||||
Function / homology | S-ADENOSYLMETHIONINE / RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Trausch, J.J. / Reyes, F.E. / Edwards, A.L. / Batey, R.T. | ||||||
![]() | ![]() Title: Structural basis for diversity in the SAM clan of riboswitches. Authors: Trausch, J.J. / Xu, Z. / Edwards, A.L. / Reyes, F.E. / Ross, P.E. / Knight, R. / Batey, R.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.3 KB | Display | ![]() |
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PDB format | ![]() | 47.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 759.6 KB | Display | ![]() |
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Full document | ![]() | 760.9 KB | Display | |
Data in XML | ![]() | 5.7 KB | Display | |
Data in CIF | ![]() | 7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 31622.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 transcription |
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#2: Chemical | ChemComp-SAM / |
#3: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 303.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1:1 mix of RNA mix and mother liquor. RNA mix contained RNA and 1 mM SAM. Mother liquor contained 50 mM Na-cacodylate, pH 7.0, 250 mM ammonium acetate, 20 mM MgCl2, and 16% 2-methyl-2,4- ...Details: 1:1 mix of RNA mix and mother liquor. RNA mix contained RNA and 1 mM SAM. Mother liquor contained 50 mM Na-cacodylate, pH 7.0, 250 mM ammonium acetate, 20 mM MgCl2, and 16% 2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 303.15K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 17, 2014 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→41.66 Å / Num. all: 14952 / Num. obs: 14916 / % possible obs: 99.8 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9 |
Reflection shell | Resolution: 3.2→3.31 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→31.408 Å
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Refine LS restraints |
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LS refinement shell |
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